Segregated
by The REAL Griffin
Summary: Samus, years after the events of Metriod:Fusion, finds that even on a team, the feeling of solitude is quite possible.
1. I told you I'd see you next mission

Several years after the events on the B.S.L Station, Samus was pardoned for what she had to do and for the damage she caused. This was mainly because the GF was getting sick of having to kill a new type of parasite every time the previous strongest was wiped out. If you thought the metroids were bad, you should have seen their predators.

Anyway, she was also given treatments shortly afterwards for the metroid DNA that was now effecting her genetics, and with enough research, she was completely cured and ready to go on more missions. What was it that vaccinated the vaccination, you may ask? Mainly a lot of controlled radiation and DNA tampering.

She was in her ship, sitting in the cockpit, parked in the Olympus, the very ship where she got mission briefing on the final part of her fight against the phazon virus. She was, coincidently, asleep in her ship, right before getting paged down to the briefing room once again by Admiral Castor Dane, only this time with the depressing realization that the fellow hunters from last time are not able to attend. She got the display, and without hesitation, she turned on her varia suit and hoped out of the hatch on the bottom of her ship. It had been a long time since she had used this ship last. This can be explained easily. On her way between the missions of destroying the phazon and her next mission, the engines failed, and it was presumed that it was internal damage to the circuitry that Ghor had done to it.

After some weapon calibrations, armor checking, and finally a system maintenance session, she was ready for briefing. Little did she know she would not be the only one going on this mission. In fact, she had a new group of three more hunters like she had before. Only this time, the three replacements were all average GF Troops.

She walked through the door and saw the slightly pleasant, slightly disappointing surprise. She would get to like these new team members, or at least she hoped she would. They were an advanced, specially trained group of the best members the GF could ever hope to have, excluding their very own Samus Aran that is.

"Ah, yes. Samus. You made it." Said the admiral, turning his attention away from the conversation he was having with one of the new members. "You have a new team, if you couldn't tell by these fine gentlemen standing here. This is Griffin," he said, pointing to the one in a green highlighted armor, "Jackson," pointing to the one he was just talking to, the man in blue highlighted armor, "and of course, Eryn," pointing to the only other female in the room, whose armor was of a slightly noticeably different physical posture than even Samus' suit. It was shorter and thinner, but other than that, it was no different then the rest of the GF standard suits.

Eryn turned to Samus. "How long has it been since you've had a female go on a mission with you?" she asked. This brought up memories of the phazon war times. That was the last time she had another huntress on her team, but she couldn't get herself to answer the question. It just wasn't leaving her head. The admiral noticed that Samus was having difficulty letting that mission go, and quickly changed the subject.

"We've got a mission to do here people. We can have time for chit-chat later." he stated, trying to get Samus' mind off of that mission. She looked up, and gave the admiral a look that told him she was ready to listen, but she was still preoccupied with the memories she had just remembered.

"Sorry sir." Said Eryn, giving her full attention to the admiral. "So what is our objective?


	2. The recovery process of Samus Aran

**Author's Notes: I will be making the chapters longer after this, this was just a chapter explaining my interpretation on how Samus got back to a semi normal position. Review at will. Enjoy!**

To further explain Samus' recovery from the metroid vaccine, we must first ask ourselves why she had it in the first place. Not long after she crashed in that astroid field and was taken to a laboratory specialized hospital, the doctors there realized that the X parasite had one predator known and on record. The metroid. Ironically, of course, this meant that Samus must become what she spent her entire career hunting. So they took DNA from a metroid, through it into a mixing bowl, and gave it to her ASAP. This caused the X inside her to benefit her. Now due to the fact that the X were actually mixing her physical being with her power armor's, she was now part metroid, part human, part Chozo, and part armor. But after her mission, she had absorbed so many X parasites, that the metroid DNA had nearly evolved. This made it impossible for the metroid DNA to sustain life, because after so much food and then starvation, it took only days for the metroid within to literally die and her regular cells and genetics filled in that which was destroyed. Because nothing on her body was so altered by the pieces of armor that it would have been unrecognizable, it was easy for them to remove all the remaining armor pieces still apart of her.

After the events on the B.S.L station, there was a major protest against her possible court-martial. The crew members upon the ship heading to the B.S.L station were more than happy to hear that she had saved them from their more than certain doom, not only from Samus, but also by Adam Malcovitch himself. Seemingly beyond the grave just to warn them that they would have died and the galaxy would become an X feeding ground if they had been infected. The crew members started the protesting of her possible court-martial, followed by anyone in the galaxy who wanted to live. Even Admiral Dane was apart of the protesting, and so, with so many protesting her and Adam, the court-martial was never even suggested


	3. You hide and I'll seek

**Author's notes: I know this chapter isn't much longer, but it left off at a good point and I was getting tired. Next chapter, I promise, will be bigger.**

"Our mission is to find out what the pirates are up to," Dane said.

"So nothing different from any other mission, right?" Eryn replied jokingly.

"True. They just never give up," he replied. "We have reason to believe that they have now decided to find a way to harness the power of the X parasite to take control of the Galactic Federation, and eventually, the galaxy. Hell, maybe even the universe if their technology gets good enough to travel that far."

"Weren't the X destroyed?" asked Jackson, ironically being on of the GF troops on the way to the B.S.L station right before it's destruction.

"The space pirates believe that they can still find a way to get to the X parasite by getting it from…" and he stopped, realizing that what he was about to say would be a touchy topic. "They believe…" he tried starting over, but then thought he should plan out the conversation a little better. He thought for a second, and then spoke. "They believe that the parasite still lives within Samus."

"How did they know about that?" Samus screamed both extremely loudly and very abruptly.

"We didn't want you to panic, Samus, so-" he started, before being cut off.

"They knew and you didn't bother to tell me? They could have intercepted and easily killed me!" she yelled. Dane hesitated to speak, in fear that he would be screamed at again.

"As far as we know, they picked up the signal of the screw attack function that we sent before you arrived. Ridley soon followed the destination and, as far as you've informed us, he was killed by the X."

"They knew the whole time?" She asked rhetorically. "No wonder you didn't court-martial me for the destruction of the station, or SR388. You didn't want word of the pirates being able to kill me when I was at my weakest to spread throughout the federation, did you!" she asked.

"You'll have to bring that up with the ones that were supervising the operation. I had nothing to do with it." He replied, apologetically.

"I… I'm sorry. I was angry, and I over reacted."

"You have every right to be angry. I'm just sorry that I couldn't contact you to warn you about the pirates." She nodded as Dane turned back to the group. The aurora unit display came on, showing the unit in a blue pixel-like three dimensional view. It started to speak.

"I'm glad to see that you are alright, Samus. We have intel on the pirate activity, leading us to believe that they are planing an attack soon," it spoke.

"Make sure to warn the fleet about this attack," he told the men running the computers in the room. "Jackson. We need you to go to the pirates closest ship, the Despair. We believe that the Despair will be the attacking ship. You will go and destroy it if possible."

This would normally seem like a strange request, but considering who they were protecting, it was worth the effort. That and the fact that he has a ship that could blow up a planet just by shooting a single round at it was a good reason to send him. This was an average mission for Jackson.

"Samus. You and the other three will be sent to a planet that we have just discovered recently. This unnamed planted it in an unmarked sector of the galaxy, and will act as a protection from the pirates. A segregated leave of protection, if you will. Eryn and Griffin will act as a secondary defense, assuming the the pirates are somehow able to locate you. This federation would crumble without you Samus, so we will do whatever necessary to stop the pirates from capturing you." Samus felt a strange sensation of isolation wash over her. She knew it was for her own good, along with the federation, but she felt it was ironic that they would hide their greatest weapon from their enemy rather that use it against them.

"We will be uploading the coordinates to each of your ships immediately. Get moving!" Dane finished. They all returned to their ships and set of for what was going to be Samus' laziest mission yet. Hiding


	4. The curious case of Eryn the hunter

On the quick arrival to this unnamed planet in an unnamed sector of the galaxy, Samus was required to report back to the admiral. She also was required to do so every 12 hours. Annoying as it was, if she did not do it, the federation would have to force he to a cell for her protection. At least on a planet, there is plenty of exploration.

To make matters worse, she was only allowed basic functionalities in her power armor. She could not have even morph ball bombs, nor charge beam. She did, however, have the varia upgrade incase of an attack. The pirates are known for discovering planets to ravage.

On the other hand, Samus liked to consider this a 3 week paid vacation to a less-than stellar, but still okay, planet. It felt, more than anything, empty. She started to check in with the admiral.

"Samus here. We have arrived to the unnamed planet safe and undetected. All hunters are present and accounted for. Next check in twelve hours. Samus out."

She wished that she could talk to someone other than an automatic recording system, but sending a small recording would be less detectable than an actual connected transmission.

"Three weeks. What the hell are we going to to all this time?" asked Griffin.

"I've got some ideas," said Jackson, in a less professional way than the rest of the hunters were hoping.

"Dude. Your a pervert. Why did they even send you on this mission?" asked Griffin. "All you do is make sexual innuendoes and "brag", or more like over compensate, about your "personal assets".

"If your so professional, why are you calling me 'dude'?" jackson replied.

"I never said you had to be professional. I just wanted you to stop being so perverted.

"I ought to slap the sh-"

"Enough!" yelled Eryn. "Both of you, shut the hell up and just sit in different corners."

Jackson and Griffin liked to compete. Jackson thought that Griffin was trying to "steal the ladies" from him, and Griffin hated that Jackson was even a part of the federation, being a womanizer wannabe. They had been in the same squad for years, and they were friends before they joined the federation, but Griffin took this responsibility seriously, and Jackson did not. He was kind of an immature person, and was also very lazy. He did things "when he wants", not when ordered or even asked.

Hours pasted and Samus was still bored as hell. She tried playing a game on her ship's interface, but to her surprise, (sarcastically of course,) it didn't work. Not even minecraft, a game thousands of years old, but never retiring, nor pac-man or pong. Sooner than she thought, however, it was time to update her CO at the fleet about the status of Operation: Isolation.

"Samus reporting. All hunters are still safe. No signs of pirate activity." she said, followed by "or no real activity at all," under her breath. "Next check in will be in twelve hou-" she said, cut off by the sound of an explosion in at a near distance to the landing site. "A code yellow is now in effect," she added, "I repeat code yellow. An explosion has just occurred near the base." She sent the message and set off to investigate.

As she got to the other hunters' ships, they also confused, raced after her to stop her.

"Samus. Stay here, Griffin and I will go see what the sound was. You just keep your pretty face right here." Jackson told her, trying to keep up but not sound too desperate. Samus turned to face him. She knew from the moment she met him that he was a sexist freak.

"You will not be seeing my 'pretty little face' any time soon. If you ever try to put your moves on me, I will personally report the 'accident' that was you death to the federation." she replied angrily. It might have been the fact that she knew none of these people and felt alone, but she was never that angry at anyone who has hit on her before.

"Fine. Compromise our mission. See if I care." Jackson replied with a snide tone.

"Samus. I hate to call Jackson right, but you must stay here," added Eryn. "In fact, I'll leave you with Griffin so that you have some backup incase something happens here while we're gone."

Samus sighed. "Fine, I'll stay here with Griffin."

"Well don't sound too excited," replied Griffin.

"Jackson, come with me." Eryn yelled to him, as she was much further ahead at that moment.

"I'd love to!" he said, again in that same sexually sarcastic tone. They left into the jungle to see if they could find the source of the noise.

"What a pervert." Griffin stated. "That man tries to get into the pants of every girl he sees. Sometimes I'm not even sure if their girls or guys." Samus chuckled a bit. "Anyway," he continued. "He was once a good man. He's just become corrupt. Samus knew the feeling of friends being corrupted with evil. She also, for Griffin's sake, hoped that Jackson wouldn't have the same fate. Having to kill a friend/ex friend would be stressful. She had to do it thrice.

"So what do you do in the federation?" Samus asked him.

"This is it. Pretty much I protect those who need to be protected for short periods of time."

"Oh. Well that seems kind of boring." she replied.

"It has it's perks. Rarely, but sometimes." Just then, they heard another explosion, this time they also heard the sound of Jackson screaming bloody murder as he ran back to the base.

"What the hell happened?" Griffin asked him, nervous to see that Eryn wasn't there with him.

"Come quick," Jackson replied. They ran to the source of the explosions. Cutting there way through the jungle until Jackson came to a stop. He dropped to his knees, and there before him, was the mangled remains of the know passed hunter Eryn


	5. When bad goes worse

_**Warning: This chapter contains disturbing descriptions. Skipping the following paragraph will not cause a loss in storyline, but if you are week stomached, you may want to skip the next paragraph.**_ I can handle blood and gore well, so I'm not sure how bad this is to most people. Read the next paragraph with caution, or skip if you don't think you can handle it. I will not be changing the age rating, for this is the only major gory paragraph I will be writing. **Also, please enjoy!**

As Jackson stayed there on his knees before the dead huntress, Samus and Griffin just stood there, both mournful and curious. The huntress lay, with a hole blown out of her center, not completely through her body, but very close. She was dead as soon as the explosion went off, which was preferable to suffering. The armor around the gouge was scorched black, and chips and small chunks of armor were imbedded into her now exposed inner flesh. Her organs were completely missing from that area, along with any blood and bone.

_**It is now safe to read again for the week of stomach. Thank you and Enjoy!**_

"This is the work of a pirate phazon bomb." Samus said. She speaking out of a daze by hallucination of Post Traumatic Stress Disorder from the other hunters' deaths, and the other hunters knew exactly what was going on with her.

"Samus, that's impossible," Griffin reminded her, "You completely destroyed the phazon,".

"No. That's what happened. I know it." Samus insisted she knew, but Griffin had to snap her out of this dilution.

"Samus. If this was phazon, there would be nothing left of her. It was a pirate bomb.

"No. It had to be-"

"Samus! Snap out of it! It was a pirate bomb. The phazon was destroyed. You killed the phazon," Griffin yelled.

"Would you both shut up for a minute!" Jackson yelled. "Goddamn it! Eryn is dead, and all you can do is try and find out why? I… I just want to go."

"Jackson… I'm sorry." Griffin replied. "It's just that we have a mission to do, and we need to keep Samus safe."

"Shut the hell up!" Jackson yelled, and ran off into the forest.

"Jackson. Wait!" Samus yelled of to him. He was too far away though.

"It's too late. He can't here you." Griffin warned her. "Come on. Let's leave him be." They walked back to base.

Griffin carried the dead huntress, walking along side Samus. Samus wasn't sure if she could handle this. She already had to kill the last group of hunters she was with. Now Eryn is dead. Would the others meet the same fate? They walked in a quiet mourning state.

When they arrived back at the landing site, they buried their lost comrade, and had a short, yet very thoughtful moment of silence. Samus had to report what had just happened, but she would save that for an hour or two. Right now, she felt she needed some time alone, and went to her ship.

Jackson ran for a bit. He looked behind him, and the others were no longer in sight. He wiped the fake emotional tears off of his face and activated his communication system, or as it was called most of the time, the ComSys. He spoke quietly, incase he was being watched.

"Hunter Samus is ready for Operation: Segregation." He turned around, and walked back to base


End file.
